Foraminifera taxonomy with DNA barcoding and morphology

The first formal classification system of the foraminifera was proposed in 1826 by d’Orbigny, and since then their identification and delineation as distinct species has been the subject of continued and active enquiry. Despite, or perhaps because of, numerous taxonomic studies spanning nearly 200 years, the current status of benthic foraminiferal taxonomy might be perceived as one of extreme confusion.

Foraminifera are well-established biomarkers of pollution in marine environments. They possess attributes of a reliable bioindicator, namely ubiquity, short life and reproductive cycles, and sensitivity to local abiotic conditions, making them highly responsive to environmental perturbations such as organic matter enrichment and physical disturbance. However, most studies have been restricted to the morphological identification and counting of hard-shelled foraminiferal species in dried sediment samples. It might come to no surprise that about 10–25% of modern benthic foraminiferal names have been suggested to be synonyms. Consequently, there are only very few established quantitative morphological frameworks enabling researchers to consistently identify and assign a specimen to a species.

In a new publication colleagues from France and Scotland attempted to combine and reconcile molecular systematics and traditional morphology-based taxonomy to come up with a new taxonomic framework that encompasses both components. They chose the suggested barcode region for foraminifera, a fragment of the small subunit ribosomal RNA (SSU rRNA) gene, in conjunction with 16 quantitative morphometric variables. As a proof of principle the researchers tested live contemporary topotypic specimens, original fossil type specimens and specimens of genetic outliers to characterize the benthic foraminiferal species Elphidium williamsoni and it obviously worked quite well:

This case study of Elphidium williamsoni highlights the importance of an integrated taxonomic approach to resolving the taxonomic complexity faced by the benthic foraminiferal community today. Since Williamson’s first description in 1858 of E. williamsoni, which he incorrectly assigned to P. umbilcatula (itself first named by Walker and Jacob in 1798 [55]), this study now presents the first clear link between morphologically characterised type material (to which the formal name E. williamsoni is directly attributable) and the unique genetic type of E. williamsoni. The taxonomic framework proposed here provides a bridge between molecular and morphological evidence, and its implementation could provide increased rigour for species identification and discovery. It also has the potential to be robust enough for new character definitions, new species and new lines of taxonomic evidence to be added in the future. If other key taxa are systematically redefined, this would provide a foundation for a transformational change to benthic foraminiferal taxonomy.